Removed API v1 (5efd58f5) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/api/v1/init.py

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openflexure_microscope/api/v1/blueprints/init.py

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		from . import camera, stage, base, plugins, task

openflexure_microscope/api/v1/blueprints/base.py

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		from openflexure_microscope.api.utilities import gen, JsonResponse
		from openflexure_microscope.api.views import MicroscopeView

		from flask import Response, Blueprint, jsonify, request
		import logging


		class StreamAPI(MicroscopeView):
		def get(self):
		"""
		Real-time MJPEG stream from the microscope camera

		.. :quickref: State; Camera stream

		:>header Accept: image/jpeg
		:>header Content-Type: image/jpeg
		:status 200: stream active
		"""
		# Restart stream worker thread
		self.microscope.camera.start_worker()

		return Response(
		gen(self.microscope.camera),
		mimetype="multipart/x-mixed-replace; boundary=frame",
		)


		class SnapshotAPI(MicroscopeView):
		def get(self):
		"""
		Single snapshot from the camera stream

		.. :quickref: State; Camera snapshot

		:>header Accept: image/jpeg
		:>header Content-Type: image/jpeg
		:status 200: stream active
		"""
		# Restart stream worker thread
		self.microscope.camera.start_worker()

		return Response(self.microscope.camera.get_frame(), mimetype="image/jpeg")


		class StateAPI(MicroscopeView):
		def get(self):
		"""
		JSON representation of the microscope object.

		.. :quickref: State; Microscope state

		Example request:

		.. sourcecode:: http

		GET /state/ HTTP/1.1
		Accept: application/json

		Example response:

		.. sourcecode:: http

		HTTP/1.1 200 OK
		Vary: Accept
		Content-Type: application/json

		{
		"camera": {
		"preview_active": false,
		"record_active": false,
		"stream_active": true
		},
		"plugin": {},
		"stage": {
		"backlash": {
		"x": 128,
		"y": 128,
		"z": 128
		},
		"position": {
		"x": -8080,
		"y": 5665,
		"z": -12600
		}
		}
		}

		:>header Accept: application/json
		:>header Content-Type: application/json
		:status 200: state available
		"""
		return jsonify(self.microscope.state)


		class ConfigAPI(MicroscopeView):
		def get(self):
		"""
		JSON representation of the microscope config.

		.. :quickref: Config; Get microscope config

		Example request:

		.. sourcecode:: http

		GET /config/ HTTP/1.1
		Accept: application/json

		Example response:

		.. sourcecode:: http

		HTTP/1.1 200 OK
		Vary: Accept
		Content-Type: application/json

		{
		"id": "0e2c6fac5421429aac67c7903107bdd8",
		"name": "docuscope-2000",
		"fov": [4100, 3146],
		"camera_settings": {
		"image_resolution": [2592, 1944],
		"numpy_resolution": [1312, 976],
		"video_resolution": [832, 624],
		"jpeg_quality": 75,
		"picamera_settings": {
		"analog_gain": 1.0,
		"digital_gain": 1.0,
		"awb_gains": [0.92578125, 2.94921875],
		"awb_mode": "off",
		"exposure_mode": "off",
		"framerate": 24.0,
		"saturation": 0,
		"shutter_speed": 5378
		},
		},
		"stage_settings": {
		"backlash": {
		"x": 256,
		"y": 256,
		"z": 0
		}
		}
		"plugins": [
		"openflexure_microscope.plugins.default.autofocus:AutofocusPlugin",
		"openflexure_microscope.plugins.default.scan:ScanPlugin",
		"openflexure_microscope.plugins.default.camera_calibration:Plugin"
		]
		}

		:>header Accept: application/json
		:>header Content-Type: application/json
		:status 200: state available
		"""
		return jsonify(self.microscope.read_settings(json_safe=True))

		def post(self):
		"""
		Modify microscope configuration

		.. :quickref: Config; Set microscope config

		Example request:

		.. sourcecode:: http

		POST /config HTTP/1.1
		Accept: application/json

		{
		"id": "0e2c6fac5421429aac67c7903107bdd8",
		"name": "docuscope-2000",
		"fov": [4100, 3146],
		"camera_settings": {
		"image_resolution": [2592, 1944],
		"numpy_resolution": [1312, 976],
		"video_resolution": [832, 624],
		"jpeg_quality": 75,
		"picamera_settings": {
		"analog_gain": 1.0,
		"digital_gain": 1.0,
		"awb_gains": [0.92578125, 2.94921875],
		"awb_mode": "off",
		"exposure_mode": "off",
		"framerate": 24.0,
		"saturation": 0,
		"shutter_speed": 5378
		},
		},
		"stage_settings": {
		"backlash": {
		"x": 256,
		"y": 256,
		"z": 0
		}
		}
		"plugins": [
		"openflexure_microscope.plugins.default.autofocus:AutofocusPlugin",
		"openflexure_microscope.plugins.default.scan:ScanPlugin",
		"openflexure_microscope.plugins.default.camera_calibration:Plugin"
		]
		}

		:>header Accept: application/json

		:<json string id: Unique string identifier of the microscope.
		:<json string name: Friendly name for the microscope
		:<json array fov: Field of view (motor steps per full width and height of frame)
		:<json json camera_settings: - image_resolution (array): Resolution of full image captures
		- numpy_resolution (array): Resolution of full numpy array captures
		- video_resolution (array): Resolution of video recordings, low res image captures, and the preview stream
		- jpeg_quality (int): Quality in which to store JPEG capture data
		- picamera_settings (json): Key-value pairs to apply directly to any attached PiCamera object
		:<json json stage_settings: - backlash (json): x, y, and z backlash compensation, in motor steps
		:<json array plugins: Array of plugin paths to load. Requires reloading the microscope object after applying

		:<header Content-Type: application/json
		:status 200: capture created

		"""
		payload = JsonResponse(request)

		logging.debug("Updating settings from POST request:")
		logging.debug(payload.json)

		self.microscope.apply_settings(payload.json)
		self.microscope.save_settings()

		return jsonify(self.microscope.read_settings(json_safe=True))


		def construct_blueprint(microscope_obj):

		blueprint = Blueprint("base_blueprint", __name__)

		blueprint.add_url_rule(
		"/stream", view_func=StreamAPI.as_view("stream", microscope=microscope_obj)
		)

		blueprint.add_url_rule(
		"/snapshot",
		view_func=SnapshotAPI.as_view("snapshot", microscope=microscope_obj),
		)

		blueprint.add_url_rule(
		"/state", view_func=StateAPI.as_view("state", microscope=microscope_obj)
		)

		blueprint.add_url_rule(
		"/config", view_func=ConfigAPI.as_view("config", microscope=microscope_obj)
		)

		return blueprint

openflexure_microscope/api/v1/blueprints/camera/init.py

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		from flask import Blueprint

		from . import capture, preview, function


		def construct_blueprint(microscope_obj):

		blueprint = Blueprint("camera_blueprint", __name__)

		# Tag routes
		blueprint.add_url_rule(
		"/capture/<capture_id>/tags",
		view_func=capture.TagsAPI.as_view("capture_tags", microscope=microscope_obj),
		)

		# Capture routes
		blueprint.add_url_rule(
		"/capture/<capture_id>/download/<filename>",
		view_func=capture.DownloadAPI.as_view(
		"capture_download", microscope=microscope_obj
		),
		)

		blueprint.add_url_rule(
		"/capture/<capture_id>/download",
		view_func=capture.DownloadRedirectAPI.as_view(
		"capture_download_redirect", microscope=microscope_obj
		),
		)

		blueprint.add_url_rule(
		"/capture/<capture_id>/",
		view_func=capture.CaptureAPI.as_view("capture", microscope=microscope_obj),
		)

		blueprint.add_url_rule(
		"/capture/",
		view_func=capture.ListAPI.as_view("capture_list", microscope=microscope_obj),
		)

		# Preview routes
		blueprint.add_url_rule(
		"/preview/<string:operation>",
		view_func=preview.GPUPreviewAPI.as_view(
		"gpu_preview", microscope=microscope_obj
		),
		)

		# Function routes
		blueprint.add_url_rule(
		"/overlay",
		view_func=function.OverlayAPI.as_view("overlay", microscope=microscope_obj),
		)

		blueprint.add_url_rule(
		"/zoom", view_func=function.ZoomAPI.as_view("zoom", microscope=microscope_obj)
		)

		return blueprint

openflexure_microscope/api/v1/blueprints/camera/capture.py

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		from openflexure_microscope.api.utilities import get_bool, JsonResponse
		from openflexure_microscope.api.views import MicroscopeView
		from openflexure_microscope.utilities import filter_dict

		from flask import jsonify, request, abort, url_for, redirect, send_file


		class ListAPI(MicroscopeView):
		def get(self):
		"""
		Get list of image captures.

		.. :quickref: Captures; Get collection of captures

		:>header Accept: application/json
		:query include_unavailable: return json representations of captures that have been completely deleted

		:>jsonarr boolean available: availability of capture data
		:>jsonarr string filename: filename of capture
		:>jsonarr string id: unique id of the capture object
		:>jsonarr boolean keep_on_disk: keep the capture file on microscope after closing
		:>jsonarr boolean locked: file locked for modifications (mostly used for video recording)
		:>jsonarr string path: path on pi storage to the capture file, if available
		:>jsonarr boolean stream: capture stored in-memory as a BytesIO stream
		:>jsonarr json uri: - download (string): api uri to the capture file download
		- state (string): api uri to the capture json representation

		:>header Content-Type: application/json
		:status 200: capture found
		:status 404: no capture found with that id
		"""
		include_unavailable = get_bool(request.args.get("include_unavailable"))

		if include_unavailable:
		captures = [image.state for image in self.microscope.camera.images]
		else:
		captures = [
		image.state
		for image in self.microscope.camera.images
		if image.state["available"]
		]

		return jsonify(captures)

		def delete(self):
		"""
		Delete all captures (not yet implemented)

		.. :quickref: Captures; Delete all captures
		"""
		for image in self.microscope.camera.images:
		image.delete()

		captures = [image.state for image in self.microscope.camera.images]

		return jsonify(captures)

		def post(self):
		"""
		Create a new image capture.

		.. :quickref: Captures; New capture

		Example request:

		.. sourcecode:: http

		POST /camera/capture HTTP/1.1
		Accept: application/json

		{
		"filename": "myfirstcapture",
		"temporary": false,
		"use_video_port": true,
		"bayer": true,
		"size": {
		"width": 640,
		"height": 480
		}
		}

		:>header Accept: application/json

		:<json string filename: filename of stored capture
		:<json boolean temporary: delete the capture file on microscope after closing
		:<json boolean use_video_port: capture still image from the video port
		:<json boolean bayer: keep raw capture data in the image file
		:<json json size: - x (int): x-axis resize
		- y (int): y-axis resize

		:>json boolean available: availability of capture data
		:>json string filename: filename of capture
		:>json string id: unique id of the capture object
		:>json boolean temporary: delete the capture file on microscope after closing
		:>json boolean locked: file locked for modifications (mostly used for video recording)
		:>json string path: path on pi storage to the capture file, if available
		:>json boolean stream: capture stored in-memory as a BytesIO stream
		:>json json uri: - download (string): api uri to the capture file download
		- state (string): api uri to the capture json representation

		:<header Content-Type: application/json
		:status 200: capture created
		"""
		payload = JsonResponse(request)

		filename = payload.param("filename")
		temporary = payload.param("temporary", default=False, convert=bool)
		use_video_port = payload.param("use_video_port", default=False, convert=bool)
		bayer = payload.param("bayer", default=True, convert=bool)
		metadata = payload.param("metadata", default={}, convert=dict)
		tags = payload.param("tags", default=[], convert=list)

		resize = payload.param("size", default=None)
		if resize:
		if ("width" in resize) and ("height" in resize):
		resize = (
		int(resize["width"]),
		int(resize["height"]),
		) # Convert dict to tuple
		else:
		abort(404)

		# Explicitally acquire lock (prevents empty files being created if lock is unavailable)
		with self.microscope.camera.lock:
		output = self.microscope.camera.new_image(
		temporary=temporary, filename=filename
		)

		self.microscope.camera.capture(
		output.file, use_video_port=use_video_port, resize=resize, bayer=bayer
		)

		# Inject system metadata
		system_metadata = {
		"microscope_settings": self.microscope.read_settings(),
		"microscope_state": self.microscope.state,
		"microscope_id": self.microscope.id,
		"microscope_name": self.microscope.name,
		}
		output.system_metadata.update(system_metadata)

		# Insert custom metadata
		output.put_metadata(metadata)

		# Insert custom tags
		output.put_tags(tags)

		return jsonify(output.state)


		class CaptureAPI(MicroscopeView):
		def get(self, capture_id):
		"""
		Get JSON representation of a capture

		.. :quickref: Capture; Get capture

		Example request:

		.. sourcecode:: http

		GET /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/ HTTP/1.1
		Accept: application/json

		Example response:

		.. sourcecode:: http

		HTTP/1.1 200 OK
		Vary: Accept
		Content-Type: application/json

		{
		"available": true,
		"bytestream": false,
		"keep_on_disk": false,
		"locked": false,
		"metadata": {
		"filename": "2018-11-16_10-21-53.jpeg",
		"id": "d0b2067abbb946f19351e075c5e7cd5b",
		"path": "capture/2018-11-16_10-21-53.jpeg",
		"time": "2018-11-16_10-21-53"
		}
		"uri": {
		"download": "/api/v1/capture/d0b2067abbb946f19351e075c5e7cd5b/download",
		"state": "/api/v1/capture/d0b2067abbb946f19351e075c5e7cd5b/"
		}
		}

		:>json boolean available: availability of capture data
		:>json string filename: filename of capture
		:>json string id: unique id of the capture object
		:>json boolean keep_on_disk: keep the capture file on microscope after closing
		:>json boolean locked: file locked for modifications (mostly used for video recording)
		:>json string path: path on pi storage to the capture file, if available
		:>json boolean stream: capture stored in-memory as a BytesIO stream
		:>json json uri: - download (string): api uri to the capture file download
		- state (string): api uri to the capture json representation

		"""
		capture_obj = self.microscope.camera.image_from_id(capture_id)

		if not capture_obj:
		return abort(404) # 404 Not Found

		# Get capture state
		capture_metadata = capture_obj.state

		# Add API routes to returned state
		uri_dict = {
		"uri": {
		"state": "{}".format(url_for(".capture", capture_id=capture_obj.id))
		}
		}

		# If available, also add download link
		if capture_metadata["available"]:
		uri_dict["uri"]["download"] = "{}download/{}".format(
		url_for(".capture", capture_id=capture_obj.id), capture_obj.filename
		)

		capture_metadata.update(uri_dict)

		return jsonify(capture_metadata)

		def delete(self, capture_id):
		"""
		Delete all capture data from the Pi, even if `keep_on_disk=true;`.

		.. :quickref: Capture; Delete capture.
		"""
		capture_obj = self.microscope.camera.image_from_id(capture_id)

		if not capture_obj:
		return abort(404) # 404 Not Found

		capture_obj.delete()

		return jsonify({"return": capture_id})

		def put(self, capture_id):
		"""
		Add arbitrary metadata to the capture

		.. :quickref: Capture; Update capture metadata

		Example request:

		.. sourcecode:: http

		PUT /camera/capture/d0b2067abbb946f19351e075c5e7cd5b HTTP/1.1
		Accept: application/json

		{
		"user_id": "ofm_1234",
		"patient_number": 1452,
		}

		:>header Accept: application/json

		:<header Content-Type: application/json
		:status 200: metadata updated
		"""

		capture_obj = self.microscope.camera.image_from_id(capture_id)

		if not capture_obj:
		return abort(404) # 404 Not Found

		data_dict = JsonResponse(request).json

		capture_obj.put_metadata(data_dict)

		capture_metadata = capture_obj.state

		return jsonify(capture_metadata)


		class DownloadRedirectAPI(MicroscopeView):
		def get(self, capture_id):
		"""
		Return image data for a capture.

		Return capture data as an image file with the requested filename.
		I.e., `/(capture_id)/download/foo.jpeg` will download the image as
		`foo.jpeg`, regardless of the capture's initially set filename.

		Route automatically redirects to download the capture under it's currently set filename.
		I.e., `/(capture_id)/download` will
		redirect to `/(capture_id)/download/(filename)`.

		.. :quickref: Capture; Download capture image

		Example request:

		.. sourcecode:: http

		GET /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/download/2018-11-20_16-04-17.jpeg HTTP/1.1
		Accept: image/jpeg

		:>header Accept: image/jpeg
		:query thumbnail: return an image thumbnail e.g. ?thumbnail=true

		:>header Content-Type: image/jpeg
		:status 200: capture data found
		:status 404: no capture found with that id

		"""
		capture_obj = self.microscope.camera.image_from_id(capture_id)

		if not capture_obj or not capture_obj.state["available"]:
		return abort(404) # 404 Not Found

		thumbnail = get_bool(request.args.get("thumbnail"))

		return redirect(
		url_for(
		".capture_download",
		capture_id=capture_id,
		filename=capture_obj.filename,
		thumbnail=thumbnail,
		),
		code=307,
		)


		class DownloadAPI(MicroscopeView):
		def get(self, capture_id, filename):

		capture_obj = self.microscope.camera.image_from_id(capture_id)

		if not capture_obj or not capture_obj.state["available"]:
		return abort(404) # 404 Not Found

		thumbnail = get_bool(request.args.get("thumbnail"))

		# If no filename is specified, redirect to the capture's currently set filename
		if not filename:
		return redirect(
		url_for(
		"capture_download",
		capture_id=capture_id,
		filename=capture_obj.filename,
		thumbnail=thumbnail,
		),
		code=307,
		)

		# Download the image data using the requested filename
		if thumbnail:
		img = capture_obj.thumbnail
		else:
		img = capture_obj.data

		return send_file(img, mimetype="image/jpeg")


		class TagsAPI(MicroscopeView):
		def get(self, capture_id):
		"""
		Return tag list for a capture.

		.. :quickref: Capture; Show capture tags

		Example request:

		.. sourcecode:: http

		GET /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/tags HTTP/1.1
		Accept: text/json

		:>header Accept: text/json

		:>header Content-Type: text/json
		:status 200: capture data found
		:status 404: no capture found with that id
		"""
		capture_obj = self.microscope.camera.image_from_id(capture_id)

		if not capture_obj or not capture_obj.state["available"]:
		return abort(404) # 404 Not Found

		metadata_tags = filter_dict(capture_obj.state, ["metadata", "tags"])

		return jsonify(metadata_tags)

		def put(self, capture_id):
		"""
		Add tags to the capture

		.. :quickref: Capture; Update capture tags

		Example request:

		.. sourcecode:: http

		PUT /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/tags HTTP/1.1
		Accept: application/json

		["tests", "mytag", "someothertag"]

		:>header Accept: application/json

		:<header Content-Type: application/json
		:status 200: metadata updated
		"""

		capture_obj = self.microscope.camera.image_from_id(capture_id)

		if not capture_obj or not capture_obj.state["available"]:
		return abort(404) # 404 Not Found

		data_dict = JsonResponse(request).json

		if type(data_dict) != list:
		return abort(400)

		capture_obj.put_tags(data_dict)

		metadata_tags = filter_dict(capture_obj.state, ["metadata", "tags"])

		return jsonify(metadata_tags)

		def delete(self, capture_id):
		"""
		Delete tags from the capture

		.. :quickref: Capture; Delete tags.

		Example request:

		.. sourcecode:: http

		DELETE /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/tags HTTP/1.1
		Accept: application/json

		["tests", "mytag"]

		:>header Accept: application/json

		:<header Content-Type: application/json
		:status 200: metadata updated
		"""
		capture_obj = self.microscope.camera.image_from_id(capture_id)

		if not capture_obj:
		return abort(404) # 404 Not Found

		data_dict = JsonResponse(request).json

		if type(data_dict) != list:
		return abort(400)

		for tag in data_dict:
		capture_obj.delete_tag(str(tag))

		metadata_tags = filter_dict(capture_obj.state, ["metadata", "tags"])

		return jsonify(metadata_tags)